phenolocrop (version 0.0.4)

logisLateDicr: Three-parameter logistic with the decrease in the late growth phase

Description

Apply a time-series model, three-parameter logistic with the decrease in the late growth phase, to the time-series trait data. This function was originally developed for the time-series data of rice canopy height. Fitting the time-series model is done by the "two-step procedure". For more information, see Taniguchi et al. (2022).

Usage

logisLateDicr(
  dat,
  x,
  y,
  returnModels = FALSE,
  start = c(d0 = 50, r = 0.05, a = 1e-04),
  upper = c(d0 = 200, r = Inf, a = 1),
  lower = c(d0 = 0, r = 0, a = 0)
)

Value

logisLateDicr function returns the vector of estimated parameter values. If returnModels = TRUE, this function also returns the cubic polynomial regression object and logistic with the decrease in the late growth phase regression object.

Arguments

dat

data.frame including date and trait (e.g. canopy height).

x

Column name (character) for the date after sowing or planting.

y

Column name (character) for the trait.

returnModels

Logical value whether to return the time-series model object. Default is F.

start

Start values to estimate 'd0', 'r' and 'a'. Default is 'c(d0 = 50, r = 0.05, a = 0.0001)'.

upper

Upper bounds to estimate 'd0', 'r' and 'a'. Default is 'c(d0 = 200, r = Inf, a = 1)'.

lower

Lower bounds to estimate 'd0', 'r' and 'a'. Default is 'c(d0 = 0, r = 0, a = 0)'.

References

S. Taniguchi et al., (2022) Prediction of heading date, culm length, and biomass from canopy-height-related parameters derived from time-series UAV observations of rice. Frontiers in Plant Science, 13:998803.

Examples

library(phenolocrop)
riceCH_eg |>
   logisLateDicr("x", "height")